The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.

91.Bonfante P, Desiro A. 2017. Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota. ISME J e-pub ahead of print 7 April 2017; http://dx.doi.org/10.1038/ismej.2017.21.

178.Henk DA, Vilgalys R. 2007. Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium. Am J Bot94:1515–1526 http://dx.doi.org/10.3732/ajb.94.9.1515. [PubMed]

201.Sánchez-García M, Matheny PB. 2017. Is the switch to an ectomycorrhizal state an evolutionary key innovation in mushroom-forming fungi? A case study in the Tricholomatineae (Agaricales). Evolution71:51–65 http://dx.doi.org/10.1111/evo.13099. [PubMed]

The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.

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The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies

Fungal tree of life. Cladogram of the kingdom Fungi based on published multi-gene and genome-scale phylogenies (11–14, 17, 18, 32, 33, 83, 98, 109, 112, 167, 168). Polytomies represent regions of the tree currently unresolved by molecular and genomic data.

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microbiolspec/5/5/FUNK-0053-2016-fig1.gif

FIGURE 1

Fungal tree of life. Cladogram of the kingdom Fungi based on published multi-gene and genome-scale phylogenies (11–14, 17, 18, 32, 33, 83, 98, 109, 112, 167, 168). Polytomies represent regions of the tree currently unresolved by molecular and genomic data.